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Open Access Genome databases

Pathway annotation and analysis with Reactome: The solute carrier class of membrane transporters

Bijay Jassal

Author Affiliations

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

Human Genomics 2011, 5:310-315  doi:10.1186/1479-7364-5-4-310

Published: 1 May 2011

Abstract

Reactome is an expert-authored, peer-reviewed knowledge base of human reactions and pathways that functions as a data-mining resource and electronic textbook. Its current release covers approximately 23 per cent of the complete human proteome from UniProt. The pathway browser, search and data-mining tools facilitate searching and visualising pathway data and the analysis of user-supplied high-throughput datasets. A catalogue of all the solute-carrier (SLC) class of transporters which have known ligands has been annotated in Reactome. Reactome provides a detailed and interactive view of this set of transport reactions. Using the example of the SLC class of transporters, we show how they can be overlaid with protein-protein interaction, protein-drug interaction and gene expression data and compared with equivalent pathways in other species, to facilitate over-representation, expression and other pathway analyses.

Keywords:
solute transport; protein-ligand interaction; protein-protein interaction; pathway analysis; gene expression analysis